Align xylitol 2-dehydrogenase (EC 1.1.1.9) (characterized)
to candidate PP_3839 PP_3839 short-chain alcohol dehydrogenase
Query= reanno::BFirm:BPHYT_RS16050 (365 letters) >FitnessBrowser__Putida:PP_3839 Length = 336 Score = 105 bits (263), Expect = 1e-27 Identities = 82/252 (32%), Positives = 120/252 (47%), Gaps = 27/252 (10%) Query: 38 ELVIRIAACGICASDCKCHSGAKMFWGGPSPWVKAPVIPGHEFFGFVEEIGEGAADHFGV 97 E ++++ CG+C +D +G +G K V+ GHE G V+E+G G + Sbjct: 26 EALLKMQCCGVCHTDLHVKNGD---FGD-----KTGVVLGHEGIGVVQEVGPGVTS---L 74 Query: 98 KMGDRV-IAEQIVPCGKCRYCKSGQYWMCEVHNIFGFQREVADGGMAEYMRIPPTAIVHK 156 K GDR +A CG C YC SG +C G+ DGGMAE + V K Sbjct: 75 KPGDRASVAWFYQGCGHCEYCNSGNETLCRDVKNSGY---TVDGGMAEACIVKADYSV-K 130 Query: 157 IPDGISLEDAAIIEPLACAIHTVNRGEVQLDDV-----VVIAGAGPLGLMMTQIAHLKTP 211 +PDG+ D+A + CA T + V++ +V + I G G LG + Q A Sbjct: 131 VPDGL---DSAAASSITCAGVTTYKA-VKISNVRPGQWIAIYGLGGLGNLALQYAKNVFN 186 Query: 212 KKLVVIDLVEERLALAREYGADVTINPKQDDALAIIHSLTDGYGCDVYIETTGAPIGVNQ 271 K++ ID+ EE+L A E GAD+ +NP +DA +I + T G + T A N Sbjct: 187 AKVIAIDVNEEQLRFASEMGADLVVNPLNEDAAKVIQAKTG--GAHAAVVTAVAKGAFNS 244 Query: 272 GMDLIRKLGRFV 283 +D +R GR V Sbjct: 245 AVDALRAGGRLV 256 Lambda K H 0.322 0.140 0.435 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 275 Number of extensions: 17 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 365 Length of database: 336 Length adjustment: 29 Effective length of query: 336 Effective length of database: 307 Effective search space: 103152 Effective search space used: 103152 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory